The Commonwealth Remuneration Tribunal says the pay rises for the positions will be phased in over the next 18 months.

The Australian Public Service Commissioner, whose job is to evaluate performance and compliance in government departments, will enjoy a package of $600,000 a year.

The average federal bureaucrat earns $81,900 while the average full-time worker earns $74,900 a year.

The packages for top public sector positions are still well below those in the private sector. The average chief executive of a top 100 company listed on the stock exchange earns $2.1 million before bonuses.

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The tribunal said the salary of the vice-chief of the Australian Defence Force will increase from $460,000 to $550,000 while the chiefs of the army, navy and air force will see their pay rise from $440,000 to $525,000.

The Australian Electoral Commissioner goes from $400,000 to $500,000, and running Old Parliament House in Canberra will be worth $325,000.

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In June the tribunal proposed increasing the AFP commissioner's package to $600,000 but has settled on the higher figure, about $12,500 a week.

"This is a significant and singular office, with close to 7000 staff and a budget of over $2 billion, responsible for a breadth of roles, including international deployments, not encompassed by state police commissioner roles," the tribunal says.

The role of the AFP commissioner has expanded because of responsibilities in the security sector such as the prevention of terrorism.

The tribunal says the new pay rates should reflect the scale and complexity of the responsibilities of senior public office holders. Salary scales should be simplified while acknowledging the need to provide adequate compensation for the often onerous duties performed.

But unions have criticised the above-inflation increases.

The assistant national secretary of the Community and Public Sector Union, Louise Persse, said the pay rises were too high in a sector characterised by budget cuts and meagre pay rises for staff.

''For a sector that's tightening its belt ensuring job cuts, and that has worked hard to get 3 per cent pay rises, pay rises of this order are a bit much,'' Ms Persse said.

''We know these people have complex and demanding roles but especially in the light of the current environment, it's a matter of proportions.''

The tribunal argued, however, that ''remuneration arrangements for the appointees to such positions will be lower than may be paid in the private sector''.

"Nonetheless, the tribunal is conscious that remuneration must be at a level sufficient to attract and retain candidates of appropriate capacity."

It added: "Significant increases have been determined for a small number of offices where there had been no comprehensive review of roles and responsibilities for many years or where recent legislative and/or policy change had had a major impact.''

This year, federal politicians were handed two pay rises, with the Prime Minister's salary rising to $495,000 - an increase of $129,000 in one year - and the Opposition Leader's package increasing to $352,000.